PyPI - treesumstats - Versions diffs - 0.2__tar.gz → 0.4__tar.gz - Mend

treesumstats 0.2tar.gz → 0.4tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (24) hide show

{treesumstats-0.2 → treesumstats-0.4}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: treesumstats
-Version: 0.2
+Version: 0.4
 Summary: Encoding phylogenetic trees with summary statistics.
 Home-page: https://github.com/evolbioinfo/treesumstats
 Author: Anna Zhukova
@@ -250,11 +250,11 @@ The top part includes times <= T/3, the middle one > T/3 and <= 2T/3, the bottom
 Implemented in [_treesumstats.subtree_sumstats.SubtreeFeatureCalculator_](treesumstats/subtree_sumstats.py).
 In some of the following statistics reshuffled subtrees are mentioned.
-To construct a _reshuffled  subtree_ of a certain kind (cherry, triplet, etc.) from a real one we keep one of its (randomly chosen) tips,
-while for each other tip from the real subtree we replace it with a tip, for which:
-    (i) the time at the beginning of its branch is as close as possible to the time at the beginning of the real tip's branch,
-    (ii) while all the tips in the reshuffled  subtree are different and
-    (iii) there are no two tips in the reshuffled  subtree that used to belong to the same real subtree of this kind
+To construct a _reshuffled  subtree_ of a certain kind (cherry, triplet, etc.) from a real one we keep one of its (randomly chosen) locally (with respect to the subtree) external node,
+while for each other locally external node from the real subtree we replace it with a node of globally (with respect to the forest) the same type (external or internal), for which:
+    (i) the time at the beginning of its branch is as close as possible to the time at the beginning of the real node's branch,
+    (ii) while all the locally external nodes in the reshuffled  subtree are different and
+    (iii) there are no two locally external nodes in the reshuffled  subtree that used to belong to the same real subtree of this kind
     (unless there were not enough tips, e.g., 8 tips in total and only 2 ladderized quartets in the forest).
 We consider the following 2-tip, 3-tip and 4-tip subtrees to calculate the summary statistics:
@@ -267,39 +267,56 @@ We consider the following 2-tip, 3-tip and 4-tip subtrees to calculate the summa
 * 4L: fully resolved ladderized quartet
 * 4B: fully resolved balanced quartet (with two cherries as children)
-In the following statistics (spanning several list positions) X must be replaced by one of the following values: 2, 3U, 3L, 4U, 4U3U1, 4U211, 4L or 4B.
+We also consider fully internal-node subtrees:
+* I: fully unresolved subtree (or size 2 or more) whose locally external nodes are globally internal sibling nodes.
-1-8. **frac_tips_in_X:** fraction of forest tips that are found in subtrees of type X.
+In the following statistics (spanning several list positions) XT must be replaced by one of the following values: 2, 3U, 3L, 4U, 4U3U1, 4U211, 4L or 4B, while X must be replaced by either I or one of the XT values.
+1-8. **frac_tips_in_XT:** fraction of forest tips that are found in subtrees of type XT.
 9. **frac_tips_in_O:** fraction of forest tips that are not part of any subtree of size 2, 3 or 4.
-10-17. **n_tips_in_X:** number of forest tips that are found in subtrees of type X.
+10-17. **n_tips_in_XT:** number of forest tips that are found in subtrees of type XT.
 18. **n_tips_in_O:** number of forest tips that are not part of any subtree of size 2, 3 or 4.
+19. **frac_inodes_with_sibling_inodes:** fraction of forest non-root internal nodes that have internal siblings.
+20. **frac_inodes_without_sibling_inodes:** fraction of forest non-root internal nodes that do not have internal siblings.
+19. **n_inodes_with_sibling_inodes:** number of forest non-root internal nodes that have internal siblings.
+20. **n_inodes_without_sibling_inodes:** number of forest non-root internal nodes that do not have internal siblings.
+21-29. **time_diff_in_X_real_mean:** mean among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+30-38. **time_diff_in_X_real_min:** minimum among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+39-47. **time_diff_in_X_real_max:** maximum among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+48-56. **time_diff_in_X_real_var:** variance among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+57-65. **time_diff_in_X_real_median:** median among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-19-26. **time_diff_in_X_real_mean:** mean among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+66-74. **time_diff_in_X_random_mean:** mean among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-27-34. **time_diff_in_X_real_min:** minimum among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+75-83. **time_diff_in_X_random_min:** minimum among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-35-42. **time_diff_in_X_real_max:** maximum among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+84-93. **time_diff_in_X_random_max:** maximum among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-43-50. **time_diff_in_X_real_var:** variance among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+94-103. **time_diff_in_X_random_var:** variance among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-51-58. **time_diff_in_X_real_median:** median among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+104-112. **time_diff_in_X_random_median:** median among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-19-26. **time_diff_in_X_random_mean:** mean among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+113-184. **time_diff_in_X_real_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-27-34. **time_diff_in_X_random_min:** minimum among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+184-255. **time_diff_in_X_random_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-35-42. **time_diff_in_X_random_max:** maximum among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+256-264. **time_diff_in_X_random_vs_real_n_less:** number of subtrees of type X whose average locally external node sampling time differences is smaller in real subtrees than in the corresponding reshuffled  ones.
-43-50. **time_diff_in_X_random_var:** variance among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+265-273. **time_diff_in_X_random_vs_real_n_more:** number of subtrees of type X whose average locally external node sampling time differences is larger in real subtrees than in the corresponding reshuffled  ones.
-51-58. **time_diff_in_X_random_median:** median among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+274-282. **time_diff_in_X_random_vs_real_frac_less:** fraction of subtrees of type X whose average locally external node sampling time differences is smaller in real subtrees than in the corresponding reshuffled  ones.
-59-122. **time_diff_in_X_real_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+283-291. **time_diff_in_X_random_vs_real_frac_more:** fraction of subtrees of type X whose average locally external node sampling time differences is larger in real subtrees than in the corresponding reshuffled  ones.
-123-186. **time_diff_in_X_random_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+292-301. **time_diff_in_X_random_vs_real_pval_less:** p-value of the sign test checking that for subtrees of type X, their average locally external node sampling time differences are indistinguishable in real subtrees and in the corresponding reshuffled  ones (the alternative hypothesis is that some real ones are smaller).
-187-194. **time_diff_in_X_random_vs_real_n_less:** p-value of the sign test checking that for subtrees of type X, their average tip sampling time differences are indistinguishable in real subtrees and in the corresponding reshuffled  ones (the alternative hypothesis is that some real ones are smaller).
+302-310. **time_diff_in_X_random_vs_real_pval_more:** p-value of the sign test checking that for subtrees of type X, their average locally external node sampling time differences are indistinguishable in real subtrees and in the corresponding reshuffled  ones (the alternative hypothesis is that some real ones are larger).
 ## Input data

{treesumstats-0.2 → treesumstats-0.4}/README.md RENAMED Viewed

@@ -228,11 +228,11 @@ The top part includes times <= T/3, the middle one > T/3 and <= 2T/3, the bottom
 Implemented in [_treesumstats.subtree_sumstats.SubtreeFeatureCalculator_](treesumstats/subtree_sumstats.py).
 In some of the following statistics reshuffled subtrees are mentioned.
-To construct a _reshuffled  subtree_ of a certain kind (cherry, triplet, etc.) from a real one we keep one of its (randomly chosen) tips,
-while for each other tip from the real subtree we replace it with a tip, for which:
-    (i) the time at the beginning of its branch is as close as possible to the time at the beginning of the real tip's branch,
-    (ii) while all the tips in the reshuffled  subtree are different and
-    (iii) there are no two tips in the reshuffled  subtree that used to belong to the same real subtree of this kind
+To construct a _reshuffled  subtree_ of a certain kind (cherry, triplet, etc.) from a real one we keep one of its (randomly chosen) locally (with respect to the subtree) external node,
+while for each other locally external node from the real subtree we replace it with a node of globally (with respect to the forest) the same type (external or internal), for which:
+    (i) the time at the beginning of its branch is as close as possible to the time at the beginning of the real node's branch,
+    (ii) while all the locally external nodes in the reshuffled  subtree are different and
+    (iii) there are no two locally external nodes in the reshuffled  subtree that used to belong to the same real subtree of this kind
     (unless there were not enough tips, e.g., 8 tips in total and only 2 ladderized quartets in the forest).
 We consider the following 2-tip, 3-tip and 4-tip subtrees to calculate the summary statistics:
@@ -245,39 +245,56 @@ We consider the following 2-tip, 3-tip and 4-tip subtrees to calculate the summa
 * 4L: fully resolved ladderized quartet
 * 4B: fully resolved balanced quartet (with two cherries as children)
-In the following statistics (spanning several list positions) X must be replaced by one of the following values: 2, 3U, 3L, 4U, 4U3U1, 4U211, 4L or 4B.
+We also consider fully internal-node subtrees:
+* I: fully unresolved subtree (or size 2 or more) whose locally external nodes are globally internal sibling nodes.
-1-8. **frac_tips_in_X:** fraction of forest tips that are found in subtrees of type X.
+In the following statistics (spanning several list positions) XT must be replaced by one of the following values: 2, 3U, 3L, 4U, 4U3U1, 4U211, 4L or 4B, while X must be replaced by either I or one of the XT values.
+1-8. **frac_tips_in_XT:** fraction of forest tips that are found in subtrees of type XT.
 9. **frac_tips_in_O:** fraction of forest tips that are not part of any subtree of size 2, 3 or 4.
-10-17. **n_tips_in_X:** number of forest tips that are found in subtrees of type X.
+10-17. **n_tips_in_XT:** number of forest tips that are found in subtrees of type XT.
 18. **n_tips_in_O:** number of forest tips that are not part of any subtree of size 2, 3 or 4.
+19. **frac_inodes_with_sibling_inodes:** fraction of forest non-root internal nodes that have internal siblings.
+20. **frac_inodes_without_sibling_inodes:** fraction of forest non-root internal nodes that do not have internal siblings.
+19. **n_inodes_with_sibling_inodes:** number of forest non-root internal nodes that have internal siblings.
+20. **n_inodes_without_sibling_inodes:** number of forest non-root internal nodes that do not have internal siblings.
+21-29. **time_diff_in_X_real_mean:** mean among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+30-38. **time_diff_in_X_real_min:** minimum among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+39-47. **time_diff_in_X_real_max:** maximum among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+48-56. **time_diff_in_X_real_var:** variance among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+57-65. **time_diff_in_X_real_median:** median among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-19-26. **time_diff_in_X_real_mean:** mean among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+66-74. **time_diff_in_X_random_mean:** mean among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-27-34. **time_diff_in_X_real_min:** minimum among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+75-83. **time_diff_in_X_random_min:** minimum among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-35-42. **time_diff_in_X_real_max:** maximum among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+84-93. **time_diff_in_X_random_max:** maximum among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-43-50. **time_diff_in_X_real_var:** variance among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+94-103. **time_diff_in_X_random_var:** variance among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-51-58. **time_diff_in_X_real_median:** median among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+104-112. **time_diff_in_X_random_median:** median among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-19-26. **time_diff_in_X_random_mean:** mean among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+113-184. **time_diff_in_X_real_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-27-34. **time_diff_in_X_random_min:** minimum among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+184-255. **time_diff_in_X_random_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-35-42. **time_diff_in_X_random_max:** maximum among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+256-264. **time_diff_in_X_random_vs_real_n_less:** number of subtrees of type X whose average locally external node sampling time differences is smaller in real subtrees than in the corresponding reshuffled  ones.
-43-50. **time_diff_in_X_random_var:** variance among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+265-273. **time_diff_in_X_random_vs_real_n_more:** number of subtrees of type X whose average locally external node sampling time differences is larger in real subtrees than in the corresponding reshuffled  ones.
-51-58. **time_diff_in_X_random_median:** median among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+274-282. **time_diff_in_X_random_vs_real_frac_less:** fraction of subtrees of type X whose average locally external node sampling time differences is smaller in real subtrees than in the corresponding reshuffled  ones.
-59-122. **time_diff_in_X_real_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+283-291. **time_diff_in_X_random_vs_real_frac_more:** fraction of subtrees of type X whose average locally external node sampling time differences is larger in real subtrees than in the corresponding reshuffled  ones.
-123-186. **time_diff_in_X_random_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+292-301. **time_diff_in_X_random_vs_real_pval_less:** p-value of the sign test checking that for subtrees of type X, their average locally external node sampling time differences are indistinguishable in real subtrees and in the corresponding reshuffled  ones (the alternative hypothesis is that some real ones are smaller).
-187-194. **time_diff_in_X_random_vs_real_n_less:** p-value of the sign test checking that for subtrees of type X, their average tip sampling time differences are indistinguishable in real subtrees and in the corresponding reshuffled  ones (the alternative hypothesis is that some real ones are smaller).
+302-310. **time_diff_in_X_random_vs_real_pval_more:** p-value of the sign test checking that for subtrees of type X, their average locally external node sampling time differences are indistinguishable in real subtrees and in the corresponding reshuffled  ones (the alternative hypothesis is that some real ones are larger).
 ## Input data

{treesumstats-0.2 → treesumstats-0.4}/setup.py RENAMED Viewed

@@ -18,7 +18,7 @@ setup(
         'Topic :: Software Development',
         'Topic :: Software Development :: Libraries :: Python Modules',
     ],
-    version='0.2',
+    version='0.4',
     description='Encoding phylogenetic trees with summary statistics.',
     author='Anna Zhukova',
     author_email='anna.zhukova@pasteur.fr',

{treesumstats-0.2 → treesumstats-0.4}/treesumstats/help.py RENAMED Viewed

@@ -30,7 +30,8 @@ def main():
     params = parser.parse_args()
     for feature_name in FeatureManager.available_features():
-        print(f'1. **{feature_name}:** {FeatureManager.help(feature_name)}')
+        # print(f'1. **{feature_name}:** {FeatureManager.help(feature_name)}')
+        print(feature_name)
 if '__main__' == __name__:

{treesumstats-0.2 → treesumstats-0.4}/treesumstats/subtree_sumstats.py RENAMED Viewed

@@ -9,7 +9,9 @@ from treesumstats.tree_manager import annotate_forest_with_time, TIME
 OTHER_CONFIGURATION_LABEL = 'O'
-TOPOLOGY_LABELS = ['2', '3U', '3L', '4U', '4U3U1', '4U211', '4L', '4B', 'O']
+TIP_TOPOLOGY_LABELS = ['2', '3U', '3L', '4U', '4U3U1', '4U211', '4L', '4B', 'O']
+INODE_LABELS = ['I']
+TOPOLOGY_LABELS = TIP_TOPOLOGY_LABELS + INODE_LABELS
 TIP = 1
@@ -32,7 +34,9 @@ CONFIG_ORDER = [TIP, CHERRY, TRIPLET_UNRESOLVED, TRIPLET_LADDER,
 TOPOLOGY_LABEL2KEY = {'2': CHERRY, '3U': TRIPLET_UNRESOLVED, '3L': TRIPLET_LADDER, '4U': QUARTET_UNRESOLVED,
                       '4U3U1': QUARTET_TRIPLET_UNRESOLVED_TIP, '4U211': QUARTET_CHERRY_TIP_TIP,
-                      '4L': QUARTET_LADDER, '4B': QUARTET_BALANCED, 'O': 1}
+                      '4L': QUARTET_LADDER, '4B': QUARTET_BALANCED, 'O': 2}
+KEY2TOPOLOGY_LABEL = {v: k for (k, v) in TOPOLOGY_LABEL2KEY.items()}
 TOPOLOGY_LABEL2N = {'2': 2, '3U': 3, '3L': 3, '4U': 4,
                     '4U3U1': 4, '4U211': 4,
@@ -43,7 +47,8 @@ TOPOLOGY_LABEL2NAME = {'2': 'cherries', '3U': 'unresolved triplets', '3L': 'reso
                        '4U3U1': 'partially resolved quartets with an unresolved triplet and a tip as children',
                        '4U211': 'partially resolved quartets with a cherry and two tips as three children',
                        '4L': 'ladderized fully resolved quartets',
-                       '4B': 'balanced quartets (with two cherries as children)'}
+                       '4B': 'balanced quartets (with two cherries as children)',
+                       'I': 'cherries or fully unresolved n-tip subtrees (n > 2) whose external nodes were internal in the global forest'}
 TIP_TIME_PERCENTILES = [1, 5, 10, 25, 75, 90, 95, 99]
@@ -71,6 +76,27 @@ def get_config2tips(forest):
                 c.del_feature(feature)
     return topo2tips
+def pick_siblings(forest, include_polytomies=True):
+    """
+    Picks internal sibling motifs in the given forest.
+    :param include_polytomies: bool, whether to include nodes with > 2 children into consideration.
+    :param forest: list(ete3.Tree), the forest of interest
+    :return: iterator of Motif motifs
+    """
+    result = []
+    for tree in forest:
+        for root in tree.traverse():
+            if root.is_leaf() or not include_polytomies and len(root.children) != 2:
+                continue
+            siblings = [_ for _ in root.children if not _.is_leaf()]
+            if len(siblings) < 2:
+                continue
+            result.append(siblings)
+    return result
 def get_reshuffled_configs(real_configs, all_tips_sorted):
     """
     Creates reshuffled configs. For each real config a reshuffled one is constructed by
@@ -135,19 +161,21 @@ def get_avg_time_diff(times):
     return 2 * diff_sum / n / (n - 1)
 class SubtreeFeatureCalculator(FeatureCalculator):
     """Computes tree topology-related summary statistics."""
     def __init__(self):
+        self._n_inodes = None
+        self._sibling_inodes = None
         self._topo2diffs = None
         self._topo2diffs_random = None
         self._all_tips = None
         self._forest = None
         self._topo2tips = None
         self._n_tips = None
-        self._topo2tips_random = None
+        self._sibling_inodes_random = None
+        self._topo2inodes_random = None
+        self._all_inodes = None
     def help(self, feature_name, *args, **kwargs):
         if 'tips_in_' in feature_name:
@@ -157,49 +185,61 @@ class SubtreeFeatureCalculator(FeatureCalculator):
                 return f'{measure} of forest tips that are not part of any subtree of size 2, 3 or 4.'
             return f'{measure} of forest tips that are found in {TOPOLOGY_LABEL2NAME[conf]}.'
+        if 'inodes_with_sibling_inodes' in feature_name:
+            measure = 'fraction' if feature_name.startswith('frac') else 'number'
+            return f'{measure} of forest non-root internal nodes that have internal node siblings.'
+        if 'inodes_without_sibling_inodes' in feature_name:
+            measure = 'fraction' if feature_name.startswith('frac') else 'number'
+            return f'{measure} of forest non-root internal nodes that do not have internal node siblings.'
         if feature_name.startswith('time_diff_in_'):
             conf = feature_name[feature_name.find('time_diff_in_') + len('time_diff_in_'):].split('_')[0]
             is_real='real' in feature_name
-            reshuffling_expl = '(To construct a reshuffled subtree of a certain kind from a real one we keep one of its (randomly chosen) tips, ' \
-                               'while for each other tip from the real subtree we replace it with a tip, for which:' \
-                               '(i) the time at the beginning of its branch is as close as possible to the time at the beginning of the real tip\'s branch, ' \
-                               '(ii) while all the tips in the reshuffled subtree are different ' \
-                               'and (iii) there are no two tips in the reshuffled subtree that used to belong to the same real subtree of this kind ' \
-                               '(unless there were not enough tips, e.g., 8 tips in total and only 2 4-tip subtrees in the forest).'
+            reshuffling_expl = '(To construct a reshuffled subtree of a certain kind from a real one we keep one of its (randomly chosen) locally external (with respect to the subtree) nodes, ' \
+                               'while for each of its other locally external node we replace it with a node of the same global type (internal or external, with respect to the global forest), for which:' \
+                               '(i) the time at the beginning of its branch is as close as possible to the time at the beginning of the real locally external node\'s branch, ' \
+                               '(ii) while all the locally external nodes in the reshuffled subtree are different ' \
+                               'and (iii) there are no two locally external nodes in the reshuffled subtree that used to belong to the same real subtree of this kind ' \
+                               '(unless there were not enough such nodes, e.g., 8 tips in total and only 2 4-tip subtrees in the forest).'
             flavour = feature_name.split('_')[-1]
             if flavour in BASIC_METRIC2FUN or 'perc' in flavour:
                 res = f'{BASIC_METRIC2HELP[flavour]}' if flavour in BASIC_METRIC2FUN \
                     else f'{re.findall(r'\d+', flavour)[0]}th percentile'
-                res += f' of average of all tip pair sampling time differences in a {TOPOLOGY_LABEL2NAME[conf]} among all {'' if is_real else 'reshuffled'}' \
+                res += f' of average of all external node pair sampling time differences in a {TOPOLOGY_LABEL2NAME[conf]} among all {'' if is_real else 'reshuffled'}' \
                        f'{TOPOLOGY_LABEL2NAME[conf]} in the forest.'
                 if not is_real:
                     res += reshuffling_expl
                 return res
             else:
-                if 'random_vs_real_n_less' in feature_name:
+                if 'random_vs_real_n_' in feature_name:
+                    less_or_more = 'smaller' if 'less' == feature_name.split('_')[-1] else 'larger'
                     return f'number of {TOPOLOGY_LABEL2NAME[conf]}, ' \
-                           'for which their average tip sampling time difference is smaller in real subtrees than ' \
+                           f'for which their average external node sampling time difference is {less_or_more} in real subtrees than ' \
                            f'in the corresponding reshuffled ones. {reshuffling_expl}'
-                elif 'random_vs_real_frac_less' in feature_name:
+                elif 'random_vs_real_frac_' in feature_name:
+                    less_or_more = 'smaller' if 'less' == feature_name.split('_')[-1] else 'larger'
                     return f'fraction of {TOPOLOGY_LABEL2NAME[conf]}, ' \
-                           'for which their average tip sampling time difference is smaller in real subtrees than ' \
+                           f'for which their average external node sampling time difference is {less_or_more} in real subtrees than ' \
                            f'in the corresponding reshuffled ones. {reshuffling_expl}'
-                elif 'random_vs_real_pval_less' in feature_name:
+                elif 'random_vs_real_pval_' in feature_name:
+                    less_or_more = 'smaller' if 'less' == feature_name.split('_')[-1] else 'larger'
                     return f'p-value of the sign test checking that for {TOPOLOGY_LABEL2NAME[conf]}, ' \
-                           'their average tip sampling time differences are indistinguishable in real subtrees and ' \
+                           'their average external node sampling time differences are indistinguishable in real subtrees and ' \
                            f'in the corresponding reshuffled ones ' \
-                           f'(the alternative hypothesis is that some real ones are smaller). {reshuffling_expl}'
+                           f'(the alternative hypothesis is that some real ones are {less_or_more}). {reshuffling_expl}'
         return None
     def feature_names(self):
         return [f'frac_tips_in_{conf}' for conf in TOPOLOGY_LABELS] \
             + [f'n_tips_in_{conf}' for conf in TOPOLOGY_LABELS] \
+            + [f'frac_inodes_{wwo}_sibling_inodes' for wwo in ('with', 'without')] \
+            + [f'n_inodes_{wwo}_sibling_inodes' for wwo in ('with', 'without')] \
             + [f'time_diff_in_{conf}_{type}_{flavour}' for type in ('real', 'random') for flavour in BASIC_ARRAY_METRICS for conf in TOPOLOGY_LABELS if conf != OTHER_CONFIGURATION_LABEL] \
             + [f'time_diff_in_{conf}_{type}_perc{p}' for type in ('real', 'random') for p in TIP_TIME_PERCENTILES for conf in TOPOLOGY_LABELS if conf != OTHER_CONFIGURATION_LABEL] \
-            + [f'time_diff_in_{conf}_random_vs_real_{metric}_less' for metric in ('n', 'frac', 'pval') for conf in TOPOLOGY_LABELS if conf != OTHER_CONFIGURATION_LABEL]
+            + [f'time_diff_in_{conf}_random_vs_real_{metric}_{how}' for metric in ('n', 'frac', 'pval') for conf in TOPOLOGY_LABELS if conf != OTHER_CONFIGURATION_LABEL for how in ('less', 'more')]
     def set_forest(self, forest, **kwargs):
         self._forest = forest
@@ -207,9 +247,13 @@ class SubtreeFeatureCalculator(FeatureCalculator):
         self._topo2tips = None
         self._n_tips = None
         self._all_tips = None
-        self._topo2tips_random = None
+        self._all_inodes = None
+        self._sibling_inodes_random = None
         self._topo2diffs = None
         self._topo2diffs_random = None
+        self._sibling_inodes = None
+        self._topo2inodes_random = None
+        self._n_inodes = None
     @property
     def n_tips(self):
@@ -217,18 +261,36 @@ class SubtreeFeatureCalculator(FeatureCalculator):
             self._n_tips = sum(len(tree) for tree in self._forest)
         return self._n_tips
+    @property
+    def n_inodes(self):
+        if self._n_inodes is None:
+            self._n_inodes = sum(sum(1 for n in tree.traverse() if not n.is_leaf() and not n.is_root()) for tree in self._forest)
+        return self._n_inodes
     def conf2tips(self, config_type, is_real=True):
         if is_real:
             if self._topo2tips is None:
                 self._topo2tips = get_config2tips(self._forest)
             return self._topo2tips[config_type]
-        if self._topo2tips_random is None:
-            self._topo2tips_random = dict()
-        if config_type not in self._topo2tips_random:
-            self._topo2tips_random[config_type] = get_reshuffled_configs(self.conf2tips(config_type, is_real=True),
-                                                                         self.all_tips)
-        return self._topo2tips_random[config_type]
+        if self._sibling_inodes_random is None:
+            self._sibling_inodes_random = dict()
+        if config_type not in self._sibling_inodes_random:
+            self._sibling_inodes_random[config_type] = get_reshuffled_configs(self.conf2tips(config_type, is_real=True),
+                                                                              self.all_tips)
+        return self._sibling_inodes_random[config_type]
+    def sibling_inodes(self, is_real=True):
+        if is_real:
+            if self._sibling_inodes is None:
+                self._sibling_inodes = pick_siblings(self._forest)
+            return self._sibling_inodes
+        if self._sibling_inodes_random is None:
+            self._sibling_inodes_random = []
+        self._sibling_inodes_random = get_reshuffled_configs(self.sibling_inodes(is_real=True), self.all_inodes)
+        return self._sibling_inodes_random
     def conf2time_diffs(self, config_type, is_real=True):
         if is_real:
@@ -254,15 +316,31 @@ class SubtreeFeatureCalculator(FeatureCalculator):
             self._all_tips = sorted([t for tree in self._forest for t in tree], key=lambda _: getattr(_, TIME) - _.dist)
         return self._all_tips
+    @property
+    def all_inodes(self):
+        if self._all_inodes is None:
+            self._all_inodes = sorted([n for tree in self._forest for n in tree.traverse() if not n.is_leaf() and not n.is_root()],
+                                     key=lambda _: getattr(_, TIME) - _.dist)
+        return self._all_inodes
     def calculate(self, feature_name, **kwargs):
         if 'tips_in_' in feature_name:
             conf = feature_name[feature_name.find('tips_in_') + len('tips_in_'):]
             denominator = self.n_tips if feature_name.startswith('frac') else 1
             return len(self.conf2tips(TOPOLOGY_LABEL2KEY[conf], is_real=True)) * TOPOLOGY_LABEL2N[conf] / denominator
+        if 'inodes_with_sibling_inodes' in feature_name:
+            denominator = self.n_inodes if feature_name.startswith('frac') else 1
+            return sum(len(_) for _ in self.sibling_inodes(is_real=True)) / denominator
+        if 'inodes_without_sibling_inodes' in feature_name:
+            denominator = self.n_inodes if feature_name.startswith('frac') else 1
+            return (self.n_inodes - sum(len(_) for _ in self.sibling_inodes(is_real=True))) / denominator
         if feature_name.startswith('time_diff_in_'):
             conf = feature_name[feature_name.find('time_diff_in_') + len('time_diff_in_'):].split('_')[0]
-            time_diffs = self.conf2time_diffs(TOPOLOGY_LABEL2KEY[conf], is_real='real' in feature_name)
+            is_real = 'real' in feature_name
+            time_diffs = self.conf2time_diffs(TOPOLOGY_LABEL2KEY[conf], is_real=is_real) \
+                if conf in TIP_TOPOLOGY_LABELS else self.sibling_inodes(is_real=is_real)
             flavour = feature_name.split('_')[-1]
@@ -273,13 +351,14 @@ class SubtreeFeatureCalculator(FeatureCalculator):
                 perc = int(re.findall(r'\d+', flavour)[0])
                 return np.percentile(time_diffs, perc) if n else 0
             else:
-                time_diffs_random = self.conf2time_diffs(TOPOLOGY_LABEL2KEY[conf], is_real=False)
-                n_random_less_than_real = (time_diffs_random < time_diffs).sum()
-                if 'random_vs_real_n_less' in feature_name:
-                    return n_random_less_than_real
-                elif 'random_vs_real_frac_less' in feature_name:
-                    return n_random_less_than_real / n if n else 0
-                elif 'random_vs_real_pval_less' in feature_name:
-                    return scipy.stats.binomtest(n_random_less_than_real, n=n, p=0.5,
-                                                 alternative='less').pvalue if n else 1
+                time_diffs_random = self.conf2time_diffs(TOPOLOGY_LABEL2KEY[conf], is_real=False) \
+                    if conf in TIP_TOPOLOGY_LABELS else self.sibling_inodes(is_real=False)
+                is_less = 'less' == feature_name.split('_')[-1]
+                n_random_vs_real = ((time_diffs_random < time_diffs) if is_less else (time_diffs_random > time_diffs)).sum()
+                if 'random_vs_real_n_' in feature_name:
+                    return n_random_vs_real
+                elif 'random_vs_real_frac_' in feature_name:
+                    return n_random_vs_real / n if n else 0
+                elif 'random_vs_real_pval_' in feature_name:
+                    return scipy.stats.binomtest(n_random_vs_real, n=n, p=0.5, alternative='less').pvalue if n else 1

{treesumstats-0.2 → treesumstats-0.4}/treesumstats.egg-info/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: treesumstats
-Version: 0.2
+Version: 0.4
 Summary: Encoding phylogenetic trees with summary statistics.
 Home-page: https://github.com/evolbioinfo/treesumstats
 Author: Anna Zhukova
@@ -250,11 +250,11 @@ The top part includes times <= T/3, the middle one > T/3 and <= 2T/3, the bottom
 Implemented in [_treesumstats.subtree_sumstats.SubtreeFeatureCalculator_](treesumstats/subtree_sumstats.py).
 In some of the following statistics reshuffled subtrees are mentioned.
-To construct a _reshuffled  subtree_ of a certain kind (cherry, triplet, etc.) from a real one we keep one of its (randomly chosen) tips,
-while for each other tip from the real subtree we replace it with a tip, for which:
-    (i) the time at the beginning of its branch is as close as possible to the time at the beginning of the real tip's branch,
-    (ii) while all the tips in the reshuffled  subtree are different and
-    (iii) there are no two tips in the reshuffled  subtree that used to belong to the same real subtree of this kind
+To construct a _reshuffled  subtree_ of a certain kind (cherry, triplet, etc.) from a real one we keep one of its (randomly chosen) locally (with respect to the subtree) external node,
+while for each other locally external node from the real subtree we replace it with a node of globally (with respect to the forest) the same type (external or internal), for which:
+    (i) the time at the beginning of its branch is as close as possible to the time at the beginning of the real node's branch,
+    (ii) while all the locally external nodes in the reshuffled  subtree are different and
+    (iii) there are no two locally external nodes in the reshuffled  subtree that used to belong to the same real subtree of this kind
     (unless there were not enough tips, e.g., 8 tips in total and only 2 ladderized quartets in the forest).
 We consider the following 2-tip, 3-tip and 4-tip subtrees to calculate the summary statistics:
@@ -267,39 +267,56 @@ We consider the following 2-tip, 3-tip and 4-tip subtrees to calculate the summa
 * 4L: fully resolved ladderized quartet
 * 4B: fully resolved balanced quartet (with two cherries as children)
-In the following statistics (spanning several list positions) X must be replaced by one of the following values: 2, 3U, 3L, 4U, 4U3U1, 4U211, 4L or 4B.
+We also consider fully internal-node subtrees:
+* I: fully unresolved subtree (or size 2 or more) whose locally external nodes are globally internal sibling nodes.
-1-8. **frac_tips_in_X:** fraction of forest tips that are found in subtrees of type X.
+In the following statistics (spanning several list positions) XT must be replaced by one of the following values: 2, 3U, 3L, 4U, 4U3U1, 4U211, 4L or 4B, while X must be replaced by either I or one of the XT values.
+1-8. **frac_tips_in_XT:** fraction of forest tips that are found in subtrees of type XT.
 9. **frac_tips_in_O:** fraction of forest tips that are not part of any subtree of size 2, 3 or 4.
-10-17. **n_tips_in_X:** number of forest tips that are found in subtrees of type X.
+10-17. **n_tips_in_XT:** number of forest tips that are found in subtrees of type XT.
 18. **n_tips_in_O:** number of forest tips that are not part of any subtree of size 2, 3 or 4.
+19. **frac_inodes_with_sibling_inodes:** fraction of forest non-root internal nodes that have internal siblings.
+20. **frac_inodes_without_sibling_inodes:** fraction of forest non-root internal nodes that do not have internal siblings.
+19. **n_inodes_with_sibling_inodes:** number of forest non-root internal nodes that have internal siblings.
+20. **n_inodes_without_sibling_inodes:** number of forest non-root internal nodes that do not have internal siblings.
+21-29. **time_diff_in_X_real_mean:** mean among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+30-38. **time_diff_in_X_real_min:** minimum among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+39-47. **time_diff_in_X_real_max:** maximum among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+48-56. **time_diff_in_X_real_var:** variance among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
+57-65. **time_diff_in_X_real_median:** median among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-19-26. **time_diff_in_X_real_mean:** mean among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+66-74. **time_diff_in_X_random_mean:** mean among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-27-34. **time_diff_in_X_real_min:** minimum among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+75-83. **time_diff_in_X_random_min:** minimum among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-35-42. **time_diff_in_X_real_max:** maximum among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+84-93. **time_diff_in_X_random_max:** maximum among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-43-50. **time_diff_in_X_real_var:** variance among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+94-103. **time_diff_in_X_random_var:** variance among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-51-58. **time_diff_in_X_real_median:** median among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+104-112. **time_diff_in_X_random_median:** median among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-19-26. **time_diff_in_X_random_mean:** mean among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+113-184. **time_diff_in_X_real_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-27-34. **time_diff_in_X_random_min:** minimum among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+184-255. **time_diff_in_X_random_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all reshuffled subtrees of type X in the forest, of average of all locally external node pair sampling time differences in the subtree.
-35-42. **time_diff_in_X_random_max:** maximum among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+256-264. **time_diff_in_X_random_vs_real_n_less:** number of subtrees of type X whose average locally external node sampling time differences is smaller in real subtrees than in the corresponding reshuffled  ones.
-43-50. **time_diff_in_X_random_var:** variance among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+265-273. **time_diff_in_X_random_vs_real_n_more:** number of subtrees of type X whose average locally external node sampling time differences is larger in real subtrees than in the corresponding reshuffled  ones.
-51-58. **time_diff_in_X_random_median:** median among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+274-282. **time_diff_in_X_random_vs_real_frac_less:** fraction of subtrees of type X whose average locally external node sampling time differences is smaller in real subtrees than in the corresponding reshuffled  ones.
-59-122. **time_diff_in_X_real_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+283-291. **time_diff_in_X_random_vs_real_frac_more:** fraction of subtrees of type X whose average locally external node sampling time differences is larger in real subtrees than in the corresponding reshuffled  ones.
-123-186. **time_diff_in_X_random_percN:** Nth percentile (where N can be 1, 5, 10, 25, 75, 90, 95 or 99) among all reshuffled subtrees of type X in the forest, of average of all tip pair sampling time differences in the subtree.
+292-301. **time_diff_in_X_random_vs_real_pval_less:** p-value of the sign test checking that for subtrees of type X, their average locally external node sampling time differences are indistinguishable in real subtrees and in the corresponding reshuffled  ones (the alternative hypothesis is that some real ones are smaller).
-187-194. **time_diff_in_X_random_vs_real_n_less:** p-value of the sign test checking that for subtrees of type X, their average tip sampling time differences are indistinguishable in real subtrees and in the corresponding reshuffled  ones (the alternative hypothesis is that some real ones are smaller).
+302-310. **time_diff_in_X_random_vs_real_pval_more:** p-value of the sign test checking that for subtrees of type X, their average locally external node sampling time differences are indistinguishable in real subtrees and in the corresponding reshuffled  ones (the alternative hypothesis is that some real ones are larger).
 ## Input data